Table 1.
Primary literature using sc-RNAseq or sn-RNAseq to assessing adult neurogenesis in the SVZ.
| Author (Year) | Species | Age | Sex | Models | Method | Platform | Analysis | Number of Cells |
|---|---|---|---|---|---|---|---|---|
| Llorens-Bobadilla et al. (2015) [4] | Mouse | 8–12 wk | M | C57BL/6 mice | SVZ wholemount digested with trypsin, whole cells sorted and frozen | Smart-seq2 | FactoMineR, Monocle, likelihood-ratio | <100–1000 |
| Dulken et al. (2017) [5] | Mouse | 3 mo | M | GFAPGFP reporter mice, datasets Llorens-Bobadilla et al. (2015) & Shin et al. (2015) |
SVZ microdissected, digested with papain, whole cells sorted and processed live | Fluidigm C1 | GBM modeling, Monocle, SCDE, GSEA | 329 |
| Basak et al. (2018) [6] | Mouse | 2 d–1 yr | F | TroyGFPiresCreER and Ki67RFP reporter mice |
SVZ wholemount enzymatically digested, whole cells sorted and processed live | CEL-seq | RaceID2, Descan, Pseudotime in TSCAN | 1465 |
| Shi et al. (2017) [7] | Mouse | 1, 24 mo | F + M | C57BL/6 mice, dataset Llorens-Bobadilla et al. (2015) |
SVZ microdissected, digested with papain, cultured as neurospheres, whole cells sorted and frozen | Smart-Seq2 | t-SNE, WGCNA, DESeq2, GO | 22 |
| Zywitza et al. (2018) [8] | Mouse | 2–4 mo | M, F, F + M | C57BL/6N mice Lrp2 KO mice, dataset Artegiani et al. (2017) |
SVZ microdissected digested with papain, whole cells processed live or methanol-fixed |
Drop-seq | Seurat, SNN-cliq, Velocyto | 9804 |
| Shah et al. (2018) [9] | Mouse | 2–6 mo | F + M | aSMA::CreERT2; R26tdTomato/Sox2GFP mice |
SVZ microdissected, digested with papain, whole cells sorted and processed live |
10× Genomics | Seurat, SCDE | 1200, 6000 |
| Kalamakis et al. (2019) [10] | Mouse | 2, 22, 23 mo | M | C57BL/6J mice and dataset from Llorens-Bobadilla et al. (2015) | SVZ wholemount digested with trypsin, whole cells sorted and frozen | Smart-Seq2 | Seurat, Monocle, clusterProfile, DESeq2 | >2000 |
| Mizrak et al. (2019) [11] | Mouse | 8–10 wk | M, F | hGFAP::CreERT;R26tdTomato mice and datasets from Llorens-Bobadilla et al. (2015), Dulken et al. (2017) | Lateral and septal SVZ wholemounts digested with papain, whole cells processed live | Drop-seq | Phenograph, GSEA, SCDE | 41,000 |
| Dulken et al. (2019) [12] | Mouse | 3, 28–29 mo | M | C57BL/6NIA mice | SVZ microdissected, digested with papain, whole cells sorted and processed live | 10× Genomics | Seurat, Enrichr | 14,685 |
| Mizrak et al. (2020) [13] | Mouse | 8–10 wk | M | hGFAP::CreERT;R26tdTomato mice ratNes::FLPOER;R26TdTomato mice | Lateral and septal SVZ wholemounts digested with papain, whole cells processed live | Drop-seq | Phenograph, SCDE | 56,000 |
| Magnusson et al. (2020) [14] | Mouse | >2 mo | M, F | Cx3::CreER;Rbpjfl/fl;R26tdTomato/YFP mice, AAV-Cre injection into Rbpjfl/fl;R26tdTomato mice, datasets from Zywitza et al. (2018), and Hochgerner et al. (2018) |
Microdissected striatum digested with papain, whole cells sorted and frozen | Smart-Seq2, 10× Genomics | Seurat, Monocle | 1393 203 |
| Borrett et al. (2020) [15] | Mouse | E–2 mo | F + M | Emx1::Cre;R26EYFP mice Nkx2.1::Cre;R26EYFP mice |
Dorsal and lateral SVZ microdissected, digested enzymatically, whole cells sorted and processed live | 10× Genomics | Seurat | >6000 |
| Nam and Capecchi (2020) [16] | Mizrak et al. (2020) dataset | Seurat | ||||||
| Xie et al. (2020) [17] | Mouse | 2 wo–15 mo | F + M | CGDGFP reporter mice, datasets from Dulken et al. (2017), Llorens-Bobadilla et al. (2015), Codega et al. (2014) | Wholemount SVZ digested with papain, whole cells sorted and processed live | Drop-seq | Seurat, Pseudotime, TFactS, String | 5600 |
| Chen et al. (2021) [18] | Mouse | 8–10 wo | M | C57BL/6J mice | Microdissected SVZ frozen, homogenized, and nuclei processed after sucrose gradient centrifugation | 10× Genomics | Seurat, GO, CellPhoneDB, Monocle | 15,754 |
| Cebrian-Silla et al. (2021) [19] | Mouse | 4–5 wo | M, F | hGFAPGFP reporter mice | Microdissected SVZ digested with papain, whole cells multiplexed, processed live | 10× Genomics | Seurat, scVelo, GO | 30,897 |
| CD1-elite mice | Anterior/posterior-dorsal/ventral SVZ microdissected SVZ frozen, homogenized, and nuclei processed after sucrose gradient centrifugation | 45,820 | ||||||
| Borrett et al. (2022) [20] | Datasets from Hochgerner et al. (2018), Borrett et al. (2020) | Seurat, Monocle, GSEA |
Abbreviations: F = female M = male, F + M = female and male samples pooled; nr= sex not reported; E = embryonic; d = days; w = weeks, mo = months; yr = years.